Well, by the time you can read this online, it will be fixed (unless you are reading a git repo!), but at the moment, my journal (up to 11 Sep) and Blog (up to 29 Aug) are only online because my setup does not overwrite all the existing files after Hugo makes the site.
I guess I need to read the docs again.
17:09 Friday 13 September 2019 JST
Okay the best I have figured out so far is that if I put _index.md files in the subdirectories of my journal/yyyy/mm directories, those entries show up.
But it was working before without those _index.md files littered everywhere. What changed??